|
| Status |
Public on Jun 27, 2007 |
| Title |
Col_ leaf_ wildtype_rep02 |
| Sample type |
genomic |
| |
|
| Source name |
leaf tissue (approx. 12th true leaf)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Columbia
|
| Biomaterial provider |
Jerzy Paszkowski
|
| Treatment protocol |
NA
|
| Growth protocol |
Plants were grown in soil under short-day conditions (8 h light/16 h dark) at 22°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Per entry, two biological replicates of leaf tissue (approx. 12th true leaf) from 9-12 plants were frozen in liquid nitrogen. DNA was CTAB extracted and isopropanol precipitated, RNase A and Proteinase K treated, re-extracted and ethanol precipitated.
|
| Label |
Two replicates per entry with 7.5 µg DNA were fragmented; end labeled, and hybridized on Affymetrix ATH1 arrays as recommended (Affymetrix).
|
| Label protocol |
Affymetrix Double standed DNA Labelling reaction.
Manufacturer's protocol, see manufacturer's web site
|
| |
|
| Hybridization protocol |
Manufacturer's protocol, see manufacturer's web site
|
| Scan protocol |
Manufacturer's protocol, see manufacturer's web site
|
| Description |
Two replicate 3 µg genomic DNA samples of 2nd generation met1-3, 4th generation met1-3 and Col-0 were sheared by sonication and methylated DNA was immunoprecipitated, as previously described (Weber et al., 2005), and amplified following the chromatin immunoprecipitation assay protocol (Affymetrix).
|
| Data processing |
The .CHP files were generated with the Affymetrix GCOS software for preliminary analysis of the methylation values. The raw .CEL files were directly used for the methylation analysis. Using the gcRMA method, background adjustments were made and background-adjusted values from the six ATH1 datasets were quantile normalized using the Bioconductor package of R. Average signal intensities were determined in log2 scale per probe set. Contrast coefficient ratios for all pair-wise comparisons were calculated as follows: met1-3 2nd/Col-0, met1-3 4th/Col-0, and met1-3 4th/met1-3 2nd. Corrections for multiple comparisons at the 5% false discovery rate (FDR) were performed and significant differences were detected using Fisher’s test. For each probe set, three outcomes (significantly hypermethylated, no difference, and significantly hypomethylated) were possible per comparison, creating 27 possible methylation profiles analyzed at the 5% FDR level.
|
| |
|
| Submission date |
Jun 25, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Jon Reinders |
| E-mail(s) |
jon.reinders@bioveg.unige.ch
|
| Phone |
+41 22 379 3029
|
| Fax |
+41 22 379 3107
|
| URL |
http://www.unige.ch/sciences/biologie/plantsciences/grpaszkowski/
|
| Organization name |
Universite de Geneve
|
| Department |
Department of Plant Biology
|
| Lab |
Laboratory of Plant Genetics
|
| Street address |
30 quai Ernest-Ansermet
|
| City |
Genève |
| State/province |
Genève |
| ZIP/Postal code |
CH-1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE8279 |
Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation |
|
| Relations |
| Reanalyzed by |
GSE119083 |
